Gromos Tutorial Pipeline¶
[1]:
import os, sys
from pygromos.utils import bash
root_dir = os.getcwd()
#if package is not installed and path not set correct - this helps you out :)
sys.path.append(root_dir+"/..")
import pygromos
from pygromos.gromos.gromosPP import GromosPP
from pygromos.gromos.gromosXX import GromosXX
from pygromos.files.coord.cnf import Cnf
from pygromos.files.trajectory.trc import Trc
gromosPP_bin = None
gromosXX_bin = None
gromPP = GromosPP(gromosPP_bin)
gromXX = GromosXX(gromosXX_bin)
project_dir = os.path.abspath(os.path.dirname(pygromos.__file__)+"/../examples/example_files/Tutorial_System")
input_dir = project_dir+"/input"
Build initial files¶
generate Topology¶
build single topologies¶
[2]:
from pygromos.data.ff import Gromos54A7
topo_dir = bash.make_folder(project_dir+'/a_topo')
## Make Cl-
sequence = "CL-"
solvent = "H2O"
top_cl = topo_dir+"/cl.top"
gromPP.make_top(in_building_block_lib_path=Gromos54A7.mtb,
in_parameter_lib_path=Gromos54A7.ifp,
in_sequence=sequence, in_solvent=solvent,out_top_path=top_cl)
## Make Peptide
sequence = "NH3+ VAL TYR ARG LYSH GLN COO-"
solvent = "H2O"
top_peptide = topo_dir+"/peptide.top"
gromPP.make_top(in_building_block_lib_path=Gromos54A7.mtb, in_parameter_lib_path=Gromos54A7.ifp,
in_sequence=sequence, in_solvent=solvent,out_top_path=top_peptide)
[2]:
'/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/peptide.top'
combine topology¶
[3]:
top_system = topo_dir+"/vac_sys.top"
gromPP.com_top(in_topo_paths=[top_peptide, top_cl], topo_multiplier=[1,2], out_top_path=top_system)
[3]:
'/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/vac_sys.top'
generate coordinates¶
[4]:
coord_dir = bash.make_folder(project_dir+"/b_coord")
in_pdb = input_dir+"/peptide.pdb"
cnf_peptide = coord_dir+"/cnf_vacuum_peptide.cnf"
cnf_peptide = gromPP.pdb2gromos(in_pdb_path=in_pdb, in_top_path=top_peptide, out_cnf_path=cnf_peptide)
Cnf(cnf_peptide).visualize()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[4]:
<py3Dmol.view at 0x7fbcea7ad290>
add hydrogens¶
[5]:
cnf_hpeptide = coord_dir+"/vacuum_hpeptide.cnf"
cnf_hpeptide = gromPP.protonate(in_cnf_path=cnf_peptide, in_top_path=top_peptide, out_cnf_path=cnf_hpeptide)
Cnf(cnf_hpeptide).visualize()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[5]:
<py3Dmol.view at 0x7fbcea271990>
cnf to pdb¶
[6]:
out_pdb = coord_dir+"/vacuum_hpeptide.pdb"
out_pdb = gromPP.frameout(in_coord_path=cnf_hpeptide, in_top_path=top_peptide, out_file_path=out_pdb,
periodic_boundary_condition="v", out_file_format="pdb", time=0)
energy minimization - Vacuum¶
[7]:
from pygromos.data.simulation_parameters_templates import template_emin_vac
from pygromos.files.gromos_system import gromos_system
out_prefix = "vacuum_emin"
vacuum_emin_dir = bash.make_folder(project_dir+"/c_"+out_prefix)
os.chdir(vacuum_emin_dir)
grom_system = gromos_system.Gromos_System(work_folder=vacuum_emin_dir,
system_name="in_"+out_prefix,
in_top_path=top_peptide,
in_cnf_path=cnf_hpeptide,
in_imd_path=template_emin_vac)
grom_system.adapt_imd()
#del grom_system.imd.POSITIONRES
grom_system.imd.BOUNDCOND.NTB = 0
grom_system.write_files()
out_emin_vacuum = vacuum_emin_dir + "/" + out_prefix
gromXX.md_run(in_imd_path=grom_system.imd.path,
in_topo_path=grom_system.top.path,
in_coord_path=grom_system.cnf.path,
out_prefix=out_emin_vacuum)
cnf_emin_vacuum = out_emin_vacuum+".cnf"
cnf_emin_vacuum
/home/bschroed/Documents/code/PyGromosTools/pygromos/files/blocks/topology_blocks.py:1692: UserWarning: SPECIAL LJ BLOCK IS NOT IMPLEMENTED!
warnings.warn("SPECIAL LJ BLOCK IS NOT IMPLEMENTED!")
==================
CHECK dependencies
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/c_vacuum_emin
Check /home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/vac_emin.imd
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/peptide.top
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/b_coord/vacuum_hpeptide.cnf
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/c_vacuum_emin
/home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/vac_emin.imd
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/peptide.top
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/b_coord/vacuum_hpeptide.cnf
All dependencies are correct!
Parsing File: imd
Parsing File: top
Parsing File: cnf
[7]:
'/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/c_vacuum_emin/vacuum_emin.cnf'
[8]:
Cnf(cnf_emin_vacuum).visualize()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[8]:
<py3Dmol.view at 0x7fbd68566210>
Solvatistation and Solvent Energy Minimization¶
build box system¶
[9]:
from pygromos.data.solvent_coordinates import spc
out_prefix = "box"
box_dir = bash.make_folder(project_dir+"/d_"+out_prefix)
cnf_box = gromPP.sim_box(in_top_path=top_peptide, in_cnf_path=cnf_emin_vacuum,in_solvent_cnf_file_path=spc,
out_cnf_path=box_dir+"/"+out_prefix+".cnf",
periodic_boundary_condition="r", minwall=0.8, threshold=0.23, rotate=True)
Cnf(cnf_box).visualize()
sim_box @topo /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/peptide.top @pbc r @pos /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/c_vacuum_emin/vacuum_emin.cnf @solvent /home/bschroed/Documents/code/PyGromosTools/pygromos/data/solvent_coordinates/spc.cnf @rotate @thresh 0.23 @minwall 0.8
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[9]:
<py3Dmol.view at 0x7fbced3ec4d0>
to pdb¶
[10]:
out_pdb = box_dir+"/"+out_prefix+".pdb"
out_pdb = gromPP.frameout(in_coord_path=cnf_box, in_top_path=top_peptide, out_file_path=out_pdb,
periodic_boundary_condition="r", out_file_format="pdb", include="ALL", time=0)
Add Ions¶
[11]:
out_prefix = "ion"
cnf_ion = gromPP.ion(in_cnf_path=cnf_box,
in_top_path=top_peptide,
out_cnf_path=box_dir+"/"+out_prefix+".cnf",
negative=[2, "CL-"],verbose=True )
Cnf(cnf_ion).visualize()
ion @topo /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/peptide.top @pos /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/d_box/box.cnf @pbc v @potential 0.8 @mindist 0.8 @negative 2 CL-
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[11]:
<py3Dmol.view at 0x7fbcea7a1790>
Energy Minimization BOX¶
[12]:
from pygromos.data.simulation_parameters_templates import template_emin
from pygromos.files.gromos_system import gromos_system
out_prefix = "box_emin"
box_emin_dir = bash.make_folder(project_dir+"/e_"+out_prefix)
os.chdir(box_emin_dir)
grom_system = gromos_system.Gromos_System(work_folder=box_emin_dir,
system_name="in_"+out_prefix,
in_top_path=top_system,
in_cnf_path=cnf_ion,
in_imd_path=template_emin)
grom_system.adapt_imd()
grom_system.imd.STEP.NSTLIM = 3000
grom_system.imd.PRINTOUT.NTPR = 300
grom_system.write_files()
cnf_reference_position = grom_system.cnf.write_refpos(box_emin_dir+"/"+out_prefix+"_refpos.rpf")
cnf_position_restraint = grom_system.cnf.write_possrespec(box_emin_dir+"/"+out_prefix+"_posres.pos", residues=list(filter(lambda x: x != "SOLV", grom_system.cnf.get_residues())))
out_emin_box = box_emin_dir + "/" + out_prefix
gromXX.md_run(in_imd_path=grom_system.imd.path,
in_topo_path=grom_system.top.path,
in_coord_path=grom_system.cnf.path,
in_refpos_path=cnf_reference_position,
in_posresspec_path=cnf_position_restraint,
out_prefix=out_emin_box, verbose=True)
cnf_emin_box =out_emin_box+".cnf"
cnf_emin_box = gromPP.frameout(in_coord_path=cnf_emin_box, in_top_path=top_system, out_file_path=cnf_emin_box,
periodic_boundary_condition="r cog", out_file_format="cnf", include="ALL", time=0)
==================
CHECK dependencies
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin
Check /home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/emin.imd
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/vac_sys.top
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/d_box/ion.cnf
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin
/home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/emin.imd
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/vac_sys.top
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/d_box/ion.cnf
All dependencies are correct!
Parsing File: imd
Parsing File: top
Parsing File: cnf
POSRES /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin_posres.pos
COMMAND: md @topo /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/vac_sys.top @conf /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/d_box/ion.cnf @input /home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/emin.imd @posresspec /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin_posres.pos @refpos /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin_refpos.rpf @fin /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin.cnf > /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin.omd
[13]:
Cnf(cnf_emin_box).visualize()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[13]:
<py3Dmol.view at 0x7fbd6a60b450>
Simulation¶
Equilibration NVP¶
To be implemented!
[14]:
from pygromos.data.simulation_parameters_templates import template_md_tut as template_md
from pygromos.files.gromos_system import gromos_system
out_prefix = "eq_NVP"
eq_NVP_dir = bash.make_folder(project_dir+"/f_"+out_prefix)
os.chdir(eq_NVP_dir)
grom_system = gromos_system.Gromos_System(work_folder=eq_NVP_dir,
system_name="in_"+out_prefix,
in_top_path=top_system,
in_cnf_path=cnf_emin_box,
in_imd_path=template_md)
grom_system.adapt_imd(not_ligand_residues="CL-")
grom_system.imd.STEP.NSTLIM = 1000
grom_system.imd.WRITETRAJ.NTWX = 10
grom_system.imd.WRITETRAJ.NTWE = 10
grom_system.imd.INITIALISE.NTIVEL = 1
grom_system.imd.INITIALISE.NTISHK = 1
grom_system.imd.INITIALISE.NTISHI = 1
grom_system.imd.INITIALISE.NTIRTC = 1
grom_system.imd.randomize_seed()
grom_system.rebase_files()
grom_system.write_files()
out_eq_NVP = eq_NVP_dir + "/" + out_prefix
gromXX.md_run(in_imd_path=grom_system.imd.path,
in_topo_path=grom_system.top.path,
in_coord_path=grom_system.cnf.path,
out_tre=True, out_trc=True,
out_prefix=out_eq_NVP)
cnf_eq_NVP = out_eq_NVP+".cnf"
cnf_eq_NVP
==================
CHECK dependencies
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/f_eq_NVP
Check /home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/md_tut.imd
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/vac_sys.top
Check /home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin.cnf
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/f_eq_NVP
/home/bschroed/Documents/code/PyGromosTools/pygromos/data/simulation_parameters_templates/md_tut.imd
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/a_topo/vac_sys.top
/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/e_box_emin/box_emin.cnf
All dependencies are correct!
Parsing File: imd
Parsing File: top
Parsing File: cnf
[14]:
'/home/bschroed/Documents/code/PyGromosTools/examples/example_files/Tutorial_System/f_eq_NVP/eq_NVP.cnf'
[15]:
cnf = Cnf(cnf_eq_NVP)
trc = Trc(out_eq_NVP+".trc")
trc.visualize(cnf)
/home/bschroed/anaconda3/envs/pygromos/lib/python3.7/site-packages/pandas/core/generic.py:2620: PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->block2_values] [items->Index(['POS_1', 'POS_2', 'POS_3', 'POS_4', 'POS_5', 'POS_6', 'POS_7', 'POS_8',
'POS_9', 'POS_10',
...
'POS_2858', 'POS_2859', 'POS_2860', 'POS_2861', 'POS_2862', 'POS_2863',
'genbox', 'length', 'angles', 'watEver'],
dtype='object', length=2867)]
encoding=encoding,
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol